I'd expect France and England to progress to the semi-finals. I'm unconvinced by Portugal - while they did play better in the Spain game, there were still a number of chances that the Spanish team should have taken, and it's quite inconceivable for this England team to play as disjointedly as Spain did on Sunday. As long as England don't give away many freekicks near their own goal (their set-piece defending has been very poor, as others have pointed out), then they should be too strong for Portugal.
Greece, well, they were very lucky to get to the quarter-finals. Good defending, true, but they were outplayed in all three games and there are bound to come unstuck sooner or later. Having said that, France appeared terribly lackadaisical in defence against both Croatia and Switzerland, so if they become over-confident for the Q-final, they could let themselves be surprised by Greece yet.
As an aside; Stormbind, I agree that the referee in the Portugal - Russia game was wrong to send the Russian keeper off. However, I think you've been watching a different tournament to the rest of us if you think generally there has been a consistent refereeing bias towards Portugal. Portugal beat Russia because they were the better team, and played better. They beat Spain because Spain didn't play at all well - their teamwork was terrible, and their tactics foolish. El Sop is right - Portugal have earned their place in the QFs.